Histone H4 is a 103-residue protein from Xenopus laevis. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P62799.
Explore in 3D Color by confidence AlphaFold DB UniProt
The mean pLDDT of this model is 89.4 (confident overall). pLDDT is AlphaFold's per-residue confidence score from 0 to 100. In MolViewer, choose the B-factor color scheme to color the model by pLDDT, because AlphaFold stores it in the B-factor column.
| pLDDT band | Meaning | Share of residues |
|---|---|---|
| Above 90 | Very high: backbone and side chains are usually accurate | 73% |
| 70 to 90 | Confident: backbone generally right | 12% |
| 50 to 70 | Low: treat with caution | 15% |
| Below 50 | Very low: often disordered regions | 1% |
What pLDDT means and how to read it
Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling
The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA
Nucleus, Chromosome
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 2HUE | X-ray | 1.7 Å | C=21-103 |
| 1KX5 | X-ray | 1.94 Å | B/F=2-103 |
| 1KX3 | X-ray | 2.0 Å | B/F=2-103 |
| 1S32 | X-ray | 2.05 Å | B/F=2-103 |
| 3UTA | X-ray | 2.07 Å | B/F=2-103 |
| 3C1B | X-ray | 2.2 Å | B/F=2-103 |
| 3UT9 | X-ray | 2.2 Å | B/F=2-103 |
| 3UTB | X-ray | 2.2 Å | B/F=2-103 |
| 6WZ5 | EM | 2.2 Å | B/F=2-103 |
| 4ZBJ | X-ray | 2.25 Å | C=21-103 |
| 8RUQ | EM | 2.29 Å | B/F=1-103 |
| 1M19 | X-ray | 2.3 Å | B/F=2-103 |
| 1P3I | X-ray | 2.3 Å | B/F=2-103 |
| 3MGR | X-ray | 2.3 Å | B/F=2-103 |
| 7TN2 | EM | 2.3 Å | B/F=2-103 |
| 8G86 | EM | 2.3 Å | B/F=2-103 |
| 9F0O | EM | 2.3 Å | B/F=21-103 |
| 5OMX | X-ray | 2.32 Å | B/F=1-103 |
| 4EO5 | X-ray | 2.35 Å | C=21-103 |
| 6YN1 | X-ray | 2.35 Å | D/I/N/S/X/c/h/m=21-103 |
Showing 20 of 371 experimental structures (best resolution first).
MolViewer loads the AlphaFold model straight from AlphaFold DB into your browser. Show it as a cartoon, color by pLDDT, measure distances and angles, and load a PDB structure next to it to compare.